In Toad for Oracle 10.6.1 , the File Compare seems to hang on "Synchronizing Text…." window
If one clicks Cancel, Text is returned but it seems to only pick up only One compare difference.
This does not happen in Toad for Oracle 9.7.2.
In Toad for Oracle 9.7.2 takes about a minute to return the comparison results.
WORKAROUND:
install Toad for Oracle 9.7.2 (in its on directory) alongside Toad for Oracle 10.6.1.
When you need to do a file compare you can use 9.7.2 and when you want to use the new features of Toad for Oracle 10.6, you can launch this version.
STATUS:
Waiting for fix in a future version of Toad for Oracle.